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- PDB-6geq: Crystal structure of Mycobacterium tuberculosis cytochrome P450 C... -

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Basic information

Entry
Database: PDB / ID: 6geq
TitleCrystal structure of Mycobacterium tuberculosis cytochrome P450 CYP121A1 in complex with Triazole Pyrazole inhibitor 14a
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / Inhibitor complex P450 / ANTIBIOTIC
Function / homology
Function and homology information


mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EW5 / PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I020160/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/I019227/1 United Kingdom
Cancer Research UKFC001060 United Kingdom
Medical Research Council (United Kingdom)FC001060 United Kingdom
Wellcome TrustFC001060 United Kingdom
Wellcome Trust104785/B/14/Z United Kingdom
CitationJournal: Chemistryopen / Year: 2019
Title: Design and Synthesis of Imidazole and Triazole Pyrazoles asMycobacterium TuberculosisCYP121A1 Inhibitors.
Authors: Kishk, S.M. / McLean, K.J. / Sood, S. / Smith, D. / Evans, J.W.D. / Helal, M.A. / Gomaa, M.S. / Salama, I. / Mostafa, S.M. / de Carvalho, L.P.S. / Levy, C.W. / Munro, A.W. / Simons, C.
History
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4705
Polymers43,3061
Non-polymers1,1644
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-68 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.447, 77.447, 264.034
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-893-

HOH

31A-948-

HOH

41A-998-

HOH

51A-1082-

HOH

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Components

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: cyp121, MT2336 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, EC: 1.14.21.9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EW5 / 1-phenyl-3-pyridin-4-yl-~{N}-(pyridin-4-ylmethyl)pyrazole-4-carboxamide


Mass: 355.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 800 nL drops with protein-to-mother liquor at a ratio of 1 to 1, by vapour diffusion in 1.5 to 2.1 M ammonium sulfate and 0.1 M sodium MES, or Cacodylate from pH 5.5 to 6.15
PH range: 5.5-6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→65.01 Å / Num. obs: 62925 / % possible obs: 99.37 % / Redundancy: 18.2 % / Biso Wilson estimate: 15.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1593 / Rpim(I) all: 0.03821 / Rrim(I) all: 0.1639 / Net I/σ(I): 11.03
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.5184 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 6138 / CC1/2: 0.946 / Rpim(I) all: 0.1231 / % possible all: 99.63

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N4G

1n4g


Resolution: 1.6→65.01 Å / SU ML: 0.1699 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.6757 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3176 5.08 %Random
Rwork0.1724 59355 --
obs0.1739 62531 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 80 590 3707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633355
X-RAY DIFFRACTIONf_angle_d0.84624599
X-RAY DIFFRACTIONf_chiral_restr0.048509
X-RAY DIFFRACTIONf_plane_restr0.0053609
X-RAY DIFFRACTIONf_dihedral_angle_d22.45922034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.28411260.21962513X-RAY DIFFRACTION99.51
1.62-1.650.22981220.21452561X-RAY DIFFRACTION99.74
1.65-1.680.24031350.20932536X-RAY DIFFRACTION99.7
1.68-1.710.27341470.21062517X-RAY DIFFRACTION99.55
1.71-1.740.27621430.21782503X-RAY DIFFRACTION99.55
1.74-1.770.22591560.19822540X-RAY DIFFRACTION99.45
1.77-1.810.24831450.19412523X-RAY DIFFRACTION99.22
1.81-1.840.23621520.1932541X-RAY DIFFRACTION99.45
1.84-1.890.25641390.1862527X-RAY DIFFRACTION99.26
1.89-1.940.20981450.17382530X-RAY DIFFRACTION99.15
1.94-1.990.1891460.17232529X-RAY DIFFRACTION99
1.99-2.050.1991230.17212555X-RAY DIFFRACTION99.37
2.05-2.110.23211360.1722553X-RAY DIFFRACTION99.48
2.11-2.190.20851370.1662554X-RAY DIFFRACTION99.08
2.19-2.280.2151430.16412581X-RAY DIFFRACTION99.09
2.28-2.380.22321320.16162534X-RAY DIFFRACTION99.07
2.38-2.50.20661230.15792608X-RAY DIFFRACTION99.38
2.5-2.660.18351380.16872613X-RAY DIFFRACTION99.6
2.66-2.870.17511380.1582600X-RAY DIFFRACTION99.1
2.87-3.150.20911410.16292617X-RAY DIFFRACTION99.32
3.15-3.610.17121280.15922672X-RAY DIFFRACTION99.54
3.61-4.550.15061420.14732721X-RAY DIFFRACTION99.51
4.55-65.060.22331390.22927X-RAY DIFFRACTION99.51

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